2zdo - Revision history

OCA at 13:32, 1 November 2023

OCA — Wed, 01 Nov 2023 13:32:26 GMT

←Older revision		Revision as of 13:32, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2zdo' size='340' side='right'caption='[[2zdo]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2zdo' size='340' side='right'caption='[[2zdo]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zdo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zdo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZDO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1xbw\|1xbw]]~~, [[~~1sqe~~\|~~1sqe]], [[2zdp\|2zdp~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>isdG ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1280~~ "~~Micrococcus aureus~~" ~~(Rosenbach 1884) Zopf 1885])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [https://pdbe.org/2zdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [https://www.ebi.ac.uk/pdbsum/2zdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdo ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [https://pdbe.org/2zdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [https://www.ebi.ac.uk/pdbsum/2zdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HDOX1_STAAN HDOX1_STAAN]] Allows bacterial pathogens to use the host heme as an iron source. Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring to the oxo-bilirubin chromophore staphylobilins (a mixture of 5-oxo-delta-bilirubin and 15-oxo-beta-bilirubin) in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.<ref>PMID:18713745</ref>	+	[https://www.uniprot.org/uniprot/HDOX1_STAAN HDOX1_STAAN] Allows bacterial pathogens to use the host heme as an iron source. Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring to the oxo-bilirubin chromophore staphylobilins (a mixture of 5-oxo-delta-bilirubin and 15-oxo-beta-bilirubin) in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.<ref>PMID:18713745</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Heme oxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lee, W C~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~Murphy, M E.P~~]]	+	[[Category: Lee WC]]
-	[[Category: ~~Reniere, M L~~]]	+	[[Category: Murphy MEP]]
-	[[Category: ~~Skaar, E P~~]]	+	[[Category: Reniere ML]]
-	[[Category: ~~Cytoplasm]]~~	+	[[Category: Skaar EP]]
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Monooxygenase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Protein-substrate complex]]~~	+
-	~~[[Category: Ruffling~~]]	+

OCA at 07:14, 10 November 2021

OCA — Wed, 10 Nov 2021 07:14:50 GMT

←Older revision		Revision as of 07:14, 10 November 2021
Line 1:		Line 1:

	==Crystal structure of IsdG-N7A in complex with hemin==		==Crystal structure of IsdG-N7A in complex with hemin==
-	<StructureSection load='2zdo' size='340' side='right' caption='[[2zdo]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2zdo' size='340' side='right'caption='[[2zdo]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zdo]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zdo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZDO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xbw\|1xbw]], [[1sqe\|1sqe]], [[2zdp\|2zdp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xbw\|1xbw]], [[1sqe\|1sqe]], [[2zdp\|2zdp]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdG ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdG ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [~~http~~://pdbe.org/2zdo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zdo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdo ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [https://pdbe.org/2zdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [https://www.ebi.ac.uk/pdbsum/2zdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/HDOX1_STAAN HDOX1_STAAN]] Allows bacterial pathogens to use the host heme as an iron source. Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring to the oxo-bilirubin chromophore staphylobilins (a mixture of 5-oxo-delta-bilirubin and 15-oxo-beta-bilirubin) in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.<ref>PMID:18713745</ref>	+	[[https://www.uniprot.org/uniprot/HDOX1_STAAN HDOX1_STAAN]] Allows bacterial pathogens to use the host heme as an iron source. Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring to the oxo-bilirubin chromophore staphylobilins (a mixture of 5-oxo-delta-bilirubin and 15-oxo-beta-bilirubin) in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.<ref>PMID:18713745</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Heme oxygenase\|Heme oxygenase]]	+	*[[Heme oxygenase 3D structures\|Heme oxygenase 3D structures]]
-	*[[Monooxygenase\|Monooxygenase]]	+	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
	*[[Tryptophan RNA-binding attenuation protein\|Tryptophan RNA-binding attenuation protein]]		*[[Tryptophan RNA-binding attenuation protein\|Tryptophan RNA-binding attenuation protein]]
	== References ==		== References ==
Line 41:		Line 41:
	</StructureSection>		</StructureSection>
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Lee, W C]]		[[Category: Lee, W C]]
	[[Category: Murphy, M E.P]]		[[Category: Murphy, M E.P]]

OCA at 07:29, 18 October 2018

OCA — Thu, 18 Oct 2018 07:29:47 GMT

←Older revision		Revision as of 07:29, 18 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of IsdG-N7A in complex with hemin==		==Crystal structure of IsdG-N7A in complex with hemin==
	<StructureSection load='2zdo' size='340' side='right' caption='[[2zdo]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2zdo' size='340' side='right' caption='[[2zdo]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [http://pdbe.org/2zdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [http://www.ebi.ac.uk/pdbsum/2zdo PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [http://pdbe.org/2zdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [http://www.ebi.ac.uk/pdbsum/2zdo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zd/2zdo_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zd/2zdo_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 33:		Line 34:
	==See Also==		==See Also==
	*[[Heme oxygenase\|Heme oxygenase]]		*[[Heme oxygenase\|Heme oxygenase]]
		+	*[[Monooxygenase\|Monooxygenase]]
	*[[Tryptophan RNA-binding attenuation protein\|Tryptophan RNA-binding attenuation protein]]		*[[Tryptophan RNA-binding attenuation protein\|Tryptophan RNA-binding attenuation protein]]
	== References ==		== References ==
Line 43:		Line 45:
	[[Category: Reniere, M L]]		[[Category: Reniere, M L]]
	[[Category: Skaar, E P]]		[[Category: Skaar, E P]]
		+	[[Category: Cytoplasm]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Iron]]		[[Category: Iron]]

OCA at 05:06, 9 February 2016

OCA — Tue, 09 Feb 2016 05:06:45 GMT

←Older revision		Revision as of 05:06, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2zdo' size='340' side='right' caption='[[2zdo]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2zdo' size='340' side='right' caption='[[2zdo]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zdo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus Staphylococcus~~ aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zdo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xbw\|1xbw]], [[1sqe\|1sqe]], [[2zdp\|2zdp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xbw\|1xbw]], [[1sqe\|1sqe]], [[2zdp\|2zdp]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 ~~Staphylococcus~~ aureus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [http://www.ebi.ac.uk/pdbsum/2zdo PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [http://pdbe.org/2zdo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [http://www.ebi.ac.uk/pdbsum/2zdo PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~ISDG_STAAN ISDG_STAAN~~]] Allows bacterial pathogens to use the host heme as an iron source. Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring to the oxo-bilirubin chromophore staphylobilins (a mixture of 5-oxo-delta-bilirubin and 15-oxo-beta-bilirubin) in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.<ref>PMID:18713745</ref>	+	[[http://www.uniprot.org/uniprot/HDOX1_STAAN HDOX1_STAAN]] Allows bacterial pathogens to use the host heme as an iron source. Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring to the oxo-bilirubin chromophore staphylobilins (a mixture of 5-oxo-delta-bilirubin and 15-oxo-beta-bilirubin) in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.<ref>PMID:18713745</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zdo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2zdo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
-	[[Category: Staphylococcus aureus]]
	[[Category: Lee, W C]]		[[Category: Lee, W C]]
	[[Category: Murphy, M E.P]]		[[Category: Murphy, M E.P]]

OCA at 04:38, 25 December 2014

OCA — Thu, 25 Dec 2014 04:38:09 GMT

←Older revision		Revision as of 04:38, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zdo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDO FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zdo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xbw\|1xbw]], [[1sqe\|1sqe]], [[2zdp\|2zdp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xbw\|1xbw]], [[1sqe\|1sqe]], [[2zdp\|2zdp]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [http://www.ebi.ac.uk/pdbsum/2zdo PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [http://www.ebi.ac.uk/pdbsum/2zdo PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ISDG_STAAN ISDG_STAAN]] Allows bacterial pathogens to use the host heme as an iron source. Catalyzes the oxidative degradation of the heme macrocyclic porphyrin ring to the oxo-bilirubin chromophore staphylobilins (a mixture of 5-oxo-delta-bilirubin and 15-oxo-beta-bilirubin) in the presence of a suitable electron donor such as ascorbate or NADPH--cytochrome P450 reductase, with subsequent release of free iron.<ref>PMID:18713745</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 39:
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
-	[[Category: Lee, W C.]]	+	[[Category: Lee, W C]]
-	[[Category: Murphy, M E.P.]]	+	[[Category: Murphy, M E.P]]
-	[[Category: Reniere, M L.]]	+	[[Category: Reniere, M L]]
-	[[Category: Skaar, E P.]]	+	[[Category: Skaar, E P]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Iron]]		[[Category: Iron]]

OCA at 10:22, 29 September 2014

OCA — Mon, 29 Sep 2014 10:22:30 GMT

←Older revision		Revision as of 10:22, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2zdo.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of IsdG-N7A in complex with hemin==
		+	<StructureSection load='2zdo' size='340' side='right' caption='[[2zdo]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zdo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xbw\|1xbw]], [[1sqe\|1sqe]], [[2zdp\|2zdp]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zdo RCSB], [http://www.ebi.ac.uk/pdbsum/2zdo PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zd/2zdo_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	IsdG and IsdI are paralogous proteins that are intracellular components of a complex heme uptake system in Staphylococcus aureus. IsdG and IsdI were shown previously to reductively degrade hemin. Crystal structures of the apoproteins show that these proteins belong to a newly identified heme degradation family distinct from canonical eukaryotic and prokaryotic heme oxygenases. Here we report the crystal structures of an inactive N7A variant of IsdG in complex with Fe(3+)-protoporphyrin IX (IsdG-hemin) and of IsdI in complex with cobalt protoporphyrin IX (IsdI-CoPPIX) to 1.8 A or better resolution. These structures show that the metalloporphyrins are buried into similar deep clefts such that the propionic acids form salt bridges to two Arg residues. His(77) (IsdG) or His(76) (IsdI), a critical residue required for activity, is coordinated to the Fe(3+) or Co(3+) atoms, respectively. The bound porphyrin rings form extensive steric interactions in the binding cleft such that the rings are highly distorted from the plane. This distortion is best described as ruffled and places the beta- and delta-meso carbons proximal to the distal oxygen-binding site. In the IsdG-hemin structure, Fe(3+) is pentacoordinate, and the distal side is occluded by the side chain of Ile(55). However, in the structure of IsdI-CoPPIX, the distal side of the CoPPIX accommodates a chloride ion in a cavity formed through a conformational change in Ile(55). The chloride ion participates in a hydrogen bond to the side chain amide of Asn(6). Together the structures suggest a reaction mechanism in which a reactive peroxide intermediate proceeds with nucleophilic oxidation at the beta- or delta-meso carbon of the hemin.

-	~~{{STRUCTURE_2zdo\| PDB=2zdo \| SCENE= }}~~	+	Ruffling of metalloporphyrins bound to IsdG and IsdI, two heme-degrading enzymes in Staphylococcus aureus.,Lee WC, Reniere ML, Skaar EP, Murphy ME J Biol Chem. 2008 Nov 7;283(45):30957-63. Epub 2008 Aug 19. PMID:18713745<ref>PMID:18713745</ref>

-	~~===Crystal structure~~ of ~~IsdG-N7A in complex with hemin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18713745}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2zdo]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Staphylococcus_aureus Staphylococcus aureus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA].~~	+

	==See Also==		==See Also==
	*[[Heme oxygenase\|Heme oxygenase]]		*[[Heme oxygenase\|Heme oxygenase]]
-		+	*[[Tryptophan RNA-binding attenuation protein\|Tryptophan RNA-binding attenuation protein]]
-	==~~Reference~~==	+	== References ==
-	<~~ref group="xtra">PMID:018713745<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]

OCA at 12:44, 20 October 2012

OCA — Sat, 20 Oct 2012 12:44:39 GMT

←Older revision		Revision as of 12:44, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2zdo]] is a 4 chain structure ~~of [[Heme oxygenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA].	+	[[2zdo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA].

	==See Also==		==See Also==

OCA: Protected "2zdo" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 09:44:47 GMT

Protected "2zdo" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:44, 26 July 2012

OCA at 09:44, 26 July 2012

OCA — Thu, 26 Jul 2012 09:44:46 GMT

←Older revision		Revision as of 09:44, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2zdo.png\|left\|200px]]		[[Image:2zdo.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zdo", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2zdo\| PDB=2zdo \| SCENE= }}		{{STRUCTURE_2zdo\| PDB=2zdo \| SCENE= }}

	===Crystal structure of IsdG-N7A in complex with hemin===		===Crystal structure of IsdG-N7A in complex with hemin===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18713745}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18713745 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18713745}}		{{ABSTRACT_PUBMED_18713745}}

	==About this Structure==		==About this Structure==
-	~~2ZDO~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA].	+	[[2zdo]] is a 4 chain structure of [[Heme oxygenase]] with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDO OCA].
		+
		+	==See Also==
		+	*[[Heme oxygenase\|Heme oxygenase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18713745~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018713745</ref><references group="xtra"/>
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
Line 30:		Line 21:
	[[Category: Reniere, M L.]]		[[Category: Reniere, M L.]]
	[[Category: Skaar, E P.]]		[[Category: Skaar, E P.]]
-	[[Category: Cytoplasm]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Iron]]		[[Category: Iron]]
Line 38:		Line 28:
	[[Category: Protein-substrate complex]]		[[Category: Protein-substrate complex]]
	[[Category: Ruffling]]		[[Category: Ruffling]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:42:41 2009''

OCA at 04:42, 17 February 2009

OCA — Tue, 17 Feb 2009 04:42:44 GMT

←Older revision		Revision as of 04:42, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	Ruffling of Metalloporphyrins Bound to IsdG and IsdI, Two Heme-degrading Enzymes in Staphylococcus aureus., Lee WC, Reniere ML, Skaar EP, Murphy ME, J Biol Chem. 2008 Nov 7;283(45):30957-63. Epub 2008 Aug 19. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18713745 18713745]~~	+	<ref group="xtra">PMID:18713745</ref><references group="xtra"/>
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
Line 39:		Line 39:
	[[Category: Ruffling]]		[[Category: Ruffling]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Nov 27 13~~:50:~~48 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:42:41 2009''